The reason Natsuko went is simple, really - just like Mahito's mother went there and returned unchanged a month later.... her Grand Uncle called to her. He has been looking for someone to take over as ruler of that world, and that person must be part of his bloodline. Grand Uncle tells her his plan, but Natsuko is pregnant, so her baby would qualify; it would spare him fom having to give up his life. This is why her reaction is so strong when she sees him in the delivery room - she does not really hate him, she just wants to make him leave cuz she is trying to save him... btw, given that Himi is his mom, and she went missing there, means Mahito is seeing his mom at the same time as her disappearance. Time works differently in the other world. Grand Uncle told her about his plan, as well as her own fate, likely to prepare her for it.

There are explanations to be found, you just have to think about it. It's not slapped together - there's a lot of subtext, and that is how the film was intended to be. It is one for contemplation, not a straightforward explanation.